amin-sagar
commented
1 year ago It seems the file /gmxMMPBSA/lib/python3.9/site-packages/parmed/amber/mdin/gbnsr6.py doesn't have alpb in the line
class gbnsr6:
def __init__(self):
self.gbnsr6 = {'b': 0.028, 'epsin': 1.0, 'epsout': 78.5, 'istrng': 0.0, 'rs': 0.52, 'dprob': 1.4, 'space': 0.5,
'arcres': 0.2, 'rbornstat': 0, 'dgij': 0, 'radiopt': 0, 'chagb': 0, 'roh': 0.586, 'tau': 1.47, 'cavity_surften': 0.005}Changing it to
class gbnsr6:
def __init__(self):
self.gbnsr6 = {'b': 0.028, 'epsin': 1.0, 'epsout': 78.5, 'istrng': 0.0, 'rs': 0.52, 'dprob': 1.4, 'space': 0.5,
'arcres': 0.2, 'rbornstat': 0, 'dgij': 0, 'radiopt': 0, 'chagb': 0, 'roh': 0.586, 'tau': 1.47, 'alpb': 1,
'cavity_surften': 0.005}seems to solve the issue.
Valdes-Tresanco-MS
Bug summary
I am trying to use gbnsr6 with the files provided in examples directory but I get an error which says. InputError: Unknown variable (alpb) in &gb! I would be really grateful for any help/suggestions.
Terminal output
gmx_MMPBSA.log
gmx_MMPBSA.log
[INFO ] Starting gmx_MMPBSA v1.6.0+4.g93515376 [DEBUG ] WDIR : /home/amin/softwares/gmx_MMPBSA/examples/GBNSR6 [DEBUG ] AMBERHOME : /home/amin/anaconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/amin/anaconda3/envs/gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0] [DEBUG ] MPI : /home/amin/anaconda3/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.3+10.ga195c7e [DEBUG ] OS PLATFORM : Linux-5.19.0-32-generic-x86_64-with-glibc2.35 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #33~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Jan 30 17:03:34 UTC 2 [DEBUG ] OS PROCESSOR : x86_64 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv [DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |Sample input file for GB calculation using GBNSR6 model [DEBUG ] |#This input file is meant to show only that gmx_MMPBSA works. [DEBUG ] |Although, we tried to use the input files as recommended in the [DEBUG ] |#Amber manual, some parameters have been changed to perform [DEBUG ] |more expensive calculations in a reasonable amount of time. [DEBUG ] |Feel free to change the parameters #according to what is better [DEBUG ] |for your system. [DEBUG ] | [DEBUG ] |&general [DEBUG ] |sys_name="GBNSR6", [DEBUG ] |startframe=1, [DEBUG ] |endframe=10, [DEBUG ] |forcefields="leaprc.protein.ff14SB" [DEBUG ] |/ [DEBUG ] | [DEBUG ] |&gbnsr6 [DEBUG ] |istrng=0.15 [DEBUG ] |/-------------------------------------------------------------- [DEBUG ] [INFO ] Checking mmpbsa.in input file... [INFO ] Checking mmpbsa.in input file...Done. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/amin/anaconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/amin/anaconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/amin/anaconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/amin/anaconda3/envs/gmxMMPBSA/bin/sander [INFO ] gbnsr6 found! Using /home/amin/anaconda3/envs/gmxMMPBSA/bin/gbnsr6 [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [INFO ] Checking external programs...Done. [INFO ] Building AMBER topologies from GROMACS files... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [DEBUG ] Running command: echo -e "name 3 GMXMMPBSA_REC\n name 4 GMXMMPBSA_LIG\n 3 | 4\n q\n" | /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f com.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx make_ndx, version 2021.3-bioconda [DEBUG ] Executable: /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/amin/anaconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/amin/softwares/gmx_MMPBSA/examples/GBNSR6 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f com.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] [DEBUG ] GROMACS reminds you: "All Work and No Play Makes Jack a Dull Boy" (The Shining) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] [DEBUG ] 0 SOLU : 608 atoms [DEBUG ] 1 SOLV : 10845 atoms [DEBUG ] 2 SYSTEM : 11453 atoms [DEBUG ] 3 SOLU_chain1 : 478 atoms [DEBUG ] 4 SOLU_chain2 : 130 atoms [DEBUG ] [DEBUG ] nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups [DEBUG ] 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues [DEBUG ] 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help [DEBUG ] 'r': residue 'res' nr 'chain' char [DEBUG ] "name": group 'case': case sensitive 'q': save and quit [DEBUG ] 'ri': residue index [DEBUG ] [DEBUG ] > [DEBUG ] [DEBUG ] > [DEBUG ] [DEBUG ] > [DEBUG ] Copied index group 3 'GMXMMPBSA_REC' [DEBUG ] Copied index group 4 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 478 130 -> 608 [DEBUG ] [DEBUG ] 5 GMXMMPBSA_REC_GMXMMPBSA_LIG: 608 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group SOLU_chain1_SOLU_chain2 (3_4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/amin/anaconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/amin/softwares/gmx_MMPBSA/examples/GBNSR6 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Group 0 ( SOLU) has 608 elements [DEBUG ] Group 1 ( SOLV) has 10845 elements [DEBUG ] Group 2 ( SYSTEM) has 11453 elements [DEBUG ] Group 3 ( GMXMMPBSA_REC) has 478 elements [DEBUG ] Group 4 ( GMXMMPBSA_LIG) has 130 elements [DEBUG ] Group 5 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 608 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of com_traj.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 1.000 Reading frame 0 time 0.000 [DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "All Work and No Play Makes Jack a Dull Boy" (The Shining) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 5: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] No receptor structure file was defined. Using ST approach... [INFO ] Using receptor structure from complex to generate AMBER topology [INFO ] Normal Receptor: Saving group SOLU_chain1 (3) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo -e "3"| /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/amin/anaconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/amin/softwares/gmx_MMPBSA/examples/GBNSR6 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Group 0 ( SOLU) has 608 elements [DEBUG ] Group 1 ( SOLV) has 10845 elements [DEBUG ] Group 2 ( SYSTEM) has 11453 elements [DEBUG ] Group 3 ( GMXMMPBSA_REC) has 478 elements [DEBUG ] Group 4 ( GMXMMPBSA_LIG) has 130 elements [DEBUG ] Group 5 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 608 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of com_traj.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 1.000 Reading frame 0 time 0.000 [DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "All Work and No Play Makes Jack a Dull Boy" (The Shining) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 3: 'GMXMMPBSA_REC' [INFO ] No ligand structure file was defined. Using ST approach... [INFO ] Using ligand structure from complex to generate AMBER topology [INFO ] Normal Ligand: Saving group SOLU_chain2 (4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo -e "4"| /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/amin/anaconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/amin/softwares/gmx_MMPBSA/examples/GBNSR6 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Group 0 ( SOLU) has 608 elements [DEBUG ] Group 1 ( SOLV) has 10845 elements [DEBUG ] Group 2 ( SYSTEM) has 11453 elements [DEBUG ] Group 3 ( GMXMMPBSA_REC) has 478 elements [DEBUG ] Group 4 ( GMXMMPBSA_LIG) has 130 elements [DEBUG ] Group 5 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 608 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of com_traj.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 1.000 Reading frame 0 time 0.000 [DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "All Work and No Play Makes Jack a Dull Boy" (The Shining) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 4: 'GMXMMPBSA_LIG' [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected Amber/OPLS force field topology format... [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f com_traj.xtc -s com.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov [DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar [DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd [DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra [DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof [DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang [DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan [DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus [DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul [DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund [DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola [DEBUG ] Szilard Pall Sander Pronk Roland Schulz [DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers [DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen [DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov [DEBUG ] and the project leaders: [DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel [DEBUG ] [DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands. [DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at [DEBUG ] Uppsala University, Stockholm University and [DEBUG ] the Royal Institute of Technology, Sweden. [DEBUG ] check out http://www.gromacs.org for more information. [DEBUG ] [DEBUG ] GROMACS is free software; you can redistribute it and/or modify it [DEBUG ] under the terms of the GNU Lesser General Public License [DEBUG ] as published by the Free Software Foundation; either version 2.1 [DEBUG ] of the License, or (at your option) any later version. [DEBUG ] [DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda [DEBUG ] Executable: /home/amin/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/amin/anaconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/amin/softwares/gmx_MMPBSA/examples/GBNSR6 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f com_traj.xtc -s com.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] Will write xtc: Compressed trajectory (portable xdr format): xtc [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Reading file com.tpr, VERSION 2022.3 (single precision) [DEBUG ] Group 0 ( SOLU) has 608 elements [DEBUG ] Group 1 ( SOLV) has 10845 elements [DEBUG ] Group 2 ( SYSTEM) has 11453 elements [DEBUG ] Group 3 ( GMXMMPBSA_REC) has 478 elements [DEBUG ] Group 4 ( GMXMMPBSA_LIG) has 130 elements [DEBUG ] Group 5 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 608 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of com_traj.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "I Need a Little Poison" (Throwing Muses) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 5: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO ] Loading and checking parameter files for compatibility...Operating system
Ubuntu
gmx_MMPBSA Version
gmx_MMPBSA v1.6.0+4.g93515376 based on MMPBSA version 16.0 and AmberTools 20
Python version
Python 3.9.15
Installation
from source (.tar.gz)